title: ME:UACC-62

status: Public on Aug 26 2009

type: RNA

city: Charlottesville

first: Jae

middle: K

last: Lee

state: VA

department: Public Health Sciences

country: USA

institute: University of Virginia

description: Gene expression data from NCI-60 cancer cell lines before drug treatment.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array HG-U133A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with RMAexpress (Robust Microarrya Analysis) using its default analysis settings and quantile normalization method.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: NCI60 cancer cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The protocols for cell culture, cell harvests, and RNA purification, and microarray studies have been described in detail elsewhere (Shankavaram, et al., manuscript in preparation).  Briefly, seed cultures of the 60 cell lines were drawn from aliquoted stocks, passaged once in T-162 flasks, and monitored frequently for degree of confluence. The medium was RPMI-1640 with phenol red, 2 mM glutamine, and 5% fetal bovine serum. For compatibility with our other profiling studies, all fetal bovine serum was obtained from the same large batches as were used by DTP for the drug screen. One day before harvest, the cells were re-fed. Attached cells were harvested at ~80% confluence, as assessed for each flask by phase microscopy. Suspended cells were harvested at ~0.5x106 cells/mL. In pilot studies, samples of medium showed no appreciable change in pH between re-feeding and harvest, and no color change in the medium was seen in any of the flasks harvested. The time from incubator to stabilization of the preparation was kept to <1 min. Total RNA was purified using the Qiagen (Valencia, CA) RNeasy Midi Kit according to manufacturer's instructions. The RNA was then quantitated spectrophotometrically and aliquoted for storage at –80oC.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: NCI-60 Cancer Cell Line transcript expression profiling on  HG-U133A GeneChip® arrays (Affymetrix, Santa Clara, CA, USA) were performed.

tag: human cancer cell line


title: ME:SK-MEL-28


title: ME:SK-MEL-2


title: OV:SK-OV-3


title: ME:LOX IMVI


title: ME:SK-MEL-5


title: ME:M14


title: LC:NCI-H522


title: PR:PC-3


title: PR:DU-145


title: LC:NCI-H322M


title: OV:OVCAR-4


title: OV:OVCAR-8


title: LC:NCI-H226


title: ME:UACC-257


title: ME:MALME-3M


title: LC:HOP-62


title: OV:IGROV1


title: LC:A549/ATCC


title: OV:OVCAR-3


title: LC:NCI-H23


title: OV:OVCAR-5


title: RE:UO-31


title: LC:NCI-H460


title: LC:HOP-92


title: LC:EKVX


title: RE:TK-10


title: RE:RXF 393


title: RE:CAKI-1


title: RE:SN12C


title: CO:HCT-15


title: RE:A498


title: RE:ACHN


title: CO:SW-620


title: CO:KM12


title: CO:COLO 205


title: CNS:U251


title: CO:HCC-2998


title: CO:HCT-116


title: CNS:SNB-19


title: CO:HT29


title: CNS:SF-268


title: CNS:SF-295


title: BR:BT-549


title: CNS:SNB-75


title: BR:T-47D


title: BR:MDA-N


title: UN:NCI/ADR-RES


title: BR:HS 578T


title: CNS:SF-539


title: BR:MDA-MB-231/ATCC


title: BR:MCF7


title: BR:MDA-MB-435


title: LE:RPMI-8226


title: LE:HL-60(TB)


title: vmcub2

description: Gene expression data from bladder cancer cell lines before drug treatment.

source_name: bladder cancer cell line

growth_protocol: For the isogenic T24T cell pair containing vector or RhoGDI2 constructs, duplicate RNA samples were generated from independent cell cultures.

treatment_protocol: Isogenic T24T cells, bladder carcinoma–derived cell lines, primary human bladder carcinomas, and normal bladder tissues were profiled on HG-U133A GeneChipTM arrays (Affymetrix, Santa Clara, CA).

tag: human bladder cancer cell line


title: vmcub3


title: LE:CCRF-CEM


title: t24tp29


title: sw1710


title: umuc9


title: LE:MOLT-4


title: LE:SR


title: mghu4


title: slt4p3


title: umuc14


title: jon


title: fl3p10


title: kidney glomerulus, LPS treated mice, 24hour post injection, biological rep5

city: Stockholm

first: ying

last: sun

address: Scheeles Vag 2

country: Sweden

institute: Karolinska Institutet

description: Gene expression data from LPS treated mice kidney glomerulus

hyb_protocol: 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G

data_processing: The data were analyzed with GCRMA package in the bioconductor project (R version 2.4.1, gcrma version 2.6.0).

organism: Mus musculus

source_name: Mouse kidney glomerulus

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix (Expression Analysis Technical Manual, Affymetrix).

extract_protocol: Extraction of total RNA was performed according to the manufacturer's instructions ( RNeasy Mini Kit (Qiagen, cat.# 74104) for kidney glomerulus)

tag: Strain

value: C57BL/6, Gender:female, Age:9 week  Tissue:kidney glomerulus


title: kidney glomerulus, LPS treated mice, 24hour post injection, biological rep4


title: bc16.1


title: LE:K-562


title: vmcub1


title: mghu3


title: kidney glomerulus, LPS treated mice, 24hour post injection, biological rep2


title: 253jlaval


title: kidney glomerulus, LPS treated mice, 24hour post injection, biological rep6


title: kidney glomerulus, LPS treated mice, 24hour post injection, biological rep3


title: kidney glomerulus, LPS treated mice, 24hour post injection, biological rep1


title: hu456


title: umuc1


title: kk47


title: kidney glomerulus, PBS treated mice, 24hour post injection, biological rep3

description: Gene expression data from PBS treated mice kidney glomerulus


title: crl2742


title: crl7833


title: 575a


title: kidney glomerulus, PBS treated mice, 24hour post injection, biological rep2


title: psi


title: umuc6


title: cubIII


title: crl7193


title: kidney glomerulus, PBS treated mice, 24hour post injection, biological rep4


title: umuc13d


title: crl2169


title: umuc3e


title: 253jbv


title: t24


title: j82


title: umuc2


title: 253jp


title: ku7


title: rt4


title: kidney glomerulus, PBS treated mice, 24hour post injection, biological rep1


title: ht1197


title: ht1376


title: RE:786-0


title: Asymptomatic hyperCKemical subject B

city: Milan

first: Marco

last: Crimi

address: Via F. Sforza, 35

department: Dept. of Neuroscience

country: Italy

institute: University of Milan

description: This patient presents a history of familial persistent moderately elevated serum Creatine Kinase levels

source_name: Skeletal muscle biopsy


title: tccsup


title: 2227_2_C0001_T0001

status: Public on Aug 13 2009

city: Tsukuba

first: Shoshi

last: Kikuchi

state: Ibaraki

address: 2-1-2 Kan-nondai

department: Molecular Genetics

country: Japan

institute: National Institute of Agrobiological Sciences

description:
Control (CH1): Rice seeds (Oryza sativa L. cv Nipponbare) were imbibed at 30 degreesC, for 3  days, then grown in soil for 24 hours. Seedlings were transferred to water for an additional 24 hours. After treatment, shoots (second leaf appeared) were harvested and frozen in liquid nitrogen for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seeds of dwarf mutant d1 of rice (Oryza sativa L. cv Nipponbare) were imbibed at 30 degreesC, for 3  days, then grown in soil for 24 hours. Seedlings were transferred to water for an additional 24 hours. After treatment, shoots (second leaf appeared) were harvested and frozen in liquid nitrogen for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Dwarf mutant d1,

organism: Oryza sativa

source_name: Control (CH1) source: Shoot (second leaf appeared) of wild type

source_name: Target (CH2) source: Shoot (second leaf appeared) of dwarf mutant d1


title: 2227_2_C0101_T0101

description:
Control (CH1): Rice seeds (Oryza sativa L. cv Nipponbare) were imbibed at 30 degreesC for 3 days, then grown in soil for 24 hours. Seedlings were transferred to 0.1 microM gibberellic acid (GA) for an additional 24 hours. After treatment, shoots were harvested and frozen in liquid nitrogen for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seeds of dwarf mutant d1 of rice (Oryza sativa L. cv Nipponbare) were imbibed at 30 degreesC for 3 days, then grown in soil for 24 hours. Seedlings were transferred to 0.1 microM gibberellic acid (GA) for an additional 24 hours. After treatment, shoots were harvested and frozen in liquid nitrogen for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Dwarf mutant d1, GA

source_name: Control (CH1) source: Shoot (second leaf appeared) of wild type treated with 0.1 microM GA for 24 hours

source_name: Target (CH2) source: Shoot (second leaf appeared) of dwarf mutant d1 treated with 0.1 microM GA for 24 hours


title: htb9


title: Asymptomatic hyperCKemical subject A


title: 2226_2_C0001_T0002

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown by open-air cultivation. Developing panicles were harvested at August for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Mutant on seed formation of rice (Oryza sativa L. cv Nipponbare) were grown by open-air cultivation. Developing panicles of the mutant plant were harvested at August for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Seed formation mutant, Developing panicle

source_name: Control (CH1) source: Developing panicles of wild type

source_name: Target (CH2) source: Developing panicle of seed formation mutant


title: 2225_1_C0001_T0001

description:
Control (CH1): Floral primordia of rice (Oryza sativa L. cv Taichung65) were harvested for RNA extraction. Purified mRNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Floral primordia of mutant dl (dl mutant: pistils were homeotically transformed into stamens) of rice (Oryza sativa L. cv Taichung65) were harvested for RNA extraction. Purified mRNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, dl mutant, Pistil, Stamen

source_name: Control (CH1) source: Floral primordia (wild type)

source_name: Target (CH2) source: Floral primordia of mutant dl


title: scaber


title: 2228_1_C0001_T0001

description:
Control (CH1): Rice callus (Oryza sativa L. cv Taichung65) were grown with Ca2+ free MS medium for 1week, then treated with fresh Ca2+free MS medium for 24 hours (all MS liquid medium containing 3% sucrose and 2mg/liter 2,4-D). The embryonic callus was initiated from scutellum tissue of dry seed that were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice callus (Oryza sativa L. cv Taichung65) were grown with Ca2+ free MS medium for 1week, then treated in MS medium containing 3mM calcium for 24 hours (all MS liquid medium containing 3% sucrose and 2mg/liter 2,4-D). The embryonic callus was initiated from scutellum tissue of dry seed that were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Signal transduction, Calcium,

source_name: Control (CH1) source: Embryonic callus treated with calcium free for 24 hours

source_name: Target (CH2) source: Embryonic callus treated with 3mM calcium for 24 hours


title: 2219_1_C0001_T0001

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were planted in soil, grown in a growth chamber under light-dark cycle regimen (16 hours of light, 160 mmol/m2/s and 8 hours of dark) at 28 degreesC, and then transferred to continuous dark conditions (28 degreesC) at the end of the dark period for 36 hours. Leaf blade at six leaf-stage of the plants were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were planted in soil, grown in a growth chamber under light-dark cycle regimen (16 hours of light, 160 mmol/m2/s and 8 hours of dark) at 28 degreesC, and then transferred to continuous dark conditions (28 degreesC) at the end of the dark period for 44 hours. Leaf blade at six leaf-stage of the plants were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Day length, Dark condition,

source_name: Control (CH1) source: Leaf blade (6 leaf-stage) grown in dark for 36 hours

source_name: Target (CH2) source: Leaf blade (6 leaf-stage) grown in dark for 44 hours


title: 2227_1_C0001_T0001

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown in paddy field. Lower part(consisted mainly of meristem zone, differentiation zone and elongation zone) of internode II and III before heading of the plants were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Dwarf mutant d1 of rice (Oryza sativa L. cv Nipponbare) were grown in paddy field. Lower part(consisted mainly of meristem zone, differentiation zone and elongation zone) of internode II and III before heading of the d1 plants were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Signal transduction, Dwarf mutant d1

source_name: Control (CH1) source: Plants (mainly of meristem zone, differentiation zone and elongation zone; internode II and III before heading) of wild type (non-treatment)

source_name: Target (CH2) source: Lower part of internode II and III before heading of dwarf mutant d1


title: 2219_2_C0101_T0101

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were planted in soil, grown in a growth chamber under light-dark cycle regimen (16 hours of light, 160 mmol/m2/s and 8 hours of dark) at 28 degreesC, and then transferred to continuous dark conditions (28 degreesC) at the end of the dark period for 40 hours. Leaf blade at 4.5 leaf-stage of the plants were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were planted in soil, grown in a growth chamber under light-dark cycle regimen (16 hours of light, 160 mmol/m2/s and 8 hours of dark) at 28 degreesC, and then transferred to continuous dark conditions (28 degreesC) at the end of the dark period for 48 hours. Leaf blade at 4.5 leaf-stage of the plants were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Day length, Dark condition,

source_name: Control (CH1) source: Leaf (4.5 leaf-stage) grown in dark for 40 hours

source_name: Target (CH2) source: Leaf blade (4.5 leaf-stage) grown in dark condition for 48hr


title: 2226_2_C0101_T0102

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown in green-house. Developing seeds from plants were harvested at 10 days after flowering for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Antisense SPK (sucrose synthase kinase) transformant of rice (Oryza sativa L. cv Nipponbare) were grown in green-house (Plant Cell 2002 14, 619). Developing seeds from transformant plants were harvested at 10 days after flowering for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Trabsgenic, Sucrose synthase kinase (SPK) , Developing seed

source_name: Control (CH1) source: Immature seed at 10 days after flowering of non-transformant

source_name: Target (CH2) source: Immature seed at 10 days after flowering of antisense SPK transformant


title: Asymptomatic hyperCKemical subject C

source_name: Skeletal muscle biopsy


title: 2220_2_C0001_T0001

description:
Control (CH1): Dehusked and sterilized seeds of rice (Oryza sativa L. cv Nipponbare) were put on agar and kept in dark for 2  days at 4 degreesC for swelling. Then, they were transferred to 28 degreesC, keeping in dark. Coleoptiles (1 to 1.5cm long) on three days after the transfer to 28 degreesC were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Dehusked and sterilized seeds of rice (Oryza sativa L. cv Nipponbare) were put on agar and kept in dark for 2  days at 4 degreesC for swelling. Then, they were transferred to 28 degreesC, keeping in dark.  After 3 days, etiolated seedlings were under the far red (FR) light for 15 min. Coleoptiles (1 to 1.5cm long) on three days after FR treatment were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Photomorphogenesis, Far red light,

source_name: Control (CH1) source: Etiolated seedlings (coleoptiles) non-treated

source_name: Target (CH2) source: Etiolated seedlings (coleoptiles) treated with far red light for 15 min


title: 2224_1_C0001_T0001

description:
Control (CH1): The last and second latest expanded leaf of 7th week plant after sowing of rice (Oryza sativa L. cv Kitaake, non transgenic) were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The last and second latest expanded leaf of 7th week plant after sowing of rice  transgenic plant (PEPC gene transgenic) were harvested for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Transgenic, Phosphoenolpyruvate carboxylase (PEPC),

source_name: Control (CH1) source: The last and second latest expanded leaf of 7th week plant after sowing (non transgenic)

source_name: Target (CH2) source: 7th week leaf after sowing of PEPC gene transgenic plant (homo-line)


title: 2220_2_C0101_T0101

description:
Control (CH1): Dehusked and sterilized seeds of rice (Oryza sativa L. cv Nipponbare) were put on agar and kept in dark for 2  days at 4 degreesC for swelling. Then, they were transferred to 28 degreesC, keeping in dark. After three days, etiolated seedlings were under the far red (FR) light for 15 min. Coleoptiles (1 to 1.5cm long) on three days after treatment were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Dehusked and sterilized seeds of  phyA mutant rice (Oryza sativa L. cv Akitakomachi) were put on agar and kept in dark for 2  days at 4 degreesC for swelling. Then, they were transferred to 28 degreesC, keeping in dark.  After 3 days, etiolated seedlings were under the far red (FR) light for 15 min. Coleoptiles (1 to 1.5cm long) on three days after FR treatment were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Photomorphogenesis, Far red light, phyA mutant

source_name: Control (CH1) source: Etiolated seedlings of wild type treated with far red light for 15 min

source_name: Target (CH2) source: Etiolated seedlings of phyA mutant treated with far red light for 15 min


title: 2218_2_C0001_T0002

description:
Control (CH1): Rice seeds (Oryza sativa L. cv Nipponbare) were sterilized  and thoroughly rinsed in sterile distilled water. Seeds were grown hydroponically in tap water for a week, and then seedlings were transferred to no nitrogen solution for two weeks. Plants were grown under a light all day, 60% relative humidity, and a temperature of 30 degreesC. Whole plant of 3-week-old rice were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice seeds (Oryza sativa L. cv Nipponbare) were sterilized  and thoroughly rinsed in sterile distilled water. Seeds were grown hydroponically in tap water for a week, and then seedlings were transferred to nitrogen defeciency condition (containing 0.3 mM ammonium) for two weeks. Plants were grown under a light all day, 60% relative humidity, and a temperature of 30 degreesC. Whole plant of 3-week-old rice were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Metabolism, Nutrient, Nitrogen-deficiency

source_name: Control (CH1) source: 3-week-old rice seedlings cultured in nutrient solutions containing no nitrogen for 2 weeks

source_name: Target (CH2) source: Whole plant 3-week-old treated with nitrogen defecient condition for 2 weeks


title: 2223_2_C0402_T0401

description:
Control (CH1): Rice (Oryza sativa L. cv Nourin8) were grown at outdoor condition in 1/5000a pot. Superior spikelets on 7 days after flowering were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Maturation defeciency mutant-1 (poor grain filling) of rice (Oryza sativa L. cv Nourin8) were grown at outdoor condition in 1/5000a pot. Superior spikelets on 7 days after flowering were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Maturation defeciency mutant, Inferior spikelets

source_name: Control (CH1) source: Plant (spikelet) at 7 days after flowering syage

source_name: Target (CH2) source: Inferior spikelets in a panicle (7days after heading) of maturation defeciency mutant-1 (poor grain filling)


title: 2226_1_C0001_T0002

description:
Control (CH1): Immature seeds (2 weeks after pollination) of rice (japonica cv. Kin-maze) were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Immature seeds (2 weeks after pollination) of endosperm mutant EM37b rice (japonica cv. Kin-maze) were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Endosperm mutant, Immature seed

source_name: Control (CH1) source: Immature seed (2 weeks after pollination), wild-type

source_name: Target (CH2) source: Immature seeds (2 weeks after pollination) of endosperm mutant EM37b


title: 2223_1_C0001_T0001

description:
Control (CH1): Rice (Oryza sativa L. cv Nourin8) were grown by conventional cultivation at paddy field. Inferior spikelets in a panicle on 13 days after heading were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Maturation defeciency mutant-1 (poor grain filling) of rice (Oryza sativa L. cv Nourin8) were grown by conventional cultivation at paddy field. Inferior spikelets in a panicle on 13 days after heading were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Maturation defeciency mutant, Inferior spikelets

source_name: Control (CH1) source: Inferior spikelets in a panicle (panicle 13 days after heading)

source_name: Target (CH2) source: Inferior spikelets in a panicle (13 days after heading) of maturation defeciency mutant-1 (poor grain filling)


title: 2218_2_C0101_T0105

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown at glass house. Seed coat+remainding part of seed on 1 day after pollination were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were grown at glass house. Endosperm  10+14 day after pollination were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Metabolism, Tissue specificity, Endosperm

source_name: Control (CH1) source: Seed coat and remainding part of seed harvested 1 day after pollination

source_name: Target (CH2) source: Endosperm 10+14 day after pollination


title: 2218_1_C0001_T0002

description:
Control (CH1): Callus-forming embryo (50 micro gram /g fresh weight glucose) after excision from endosperm of 1-week-growth rice seed (Oryza sativa L. cv Notohikari) with 2,4-D that were harveted for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Callus-forming embryo (3 micro gram /g fresh weight glucose) of rice seed (Oryza sativa L. cv Notohikari) after excision from endosperm were grown with 2,4-D for 5 days. Then, they were trasfered to low sugar condition (sugar-free medium, see FEBS Letter 1998 428: 275). After 2 days treatment under low sugar condition, they were harveted for RNA extraction Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Metabolism, Sugar-deficiency, Metabolism

source_name: Control (CH1) source: Callus-forming embryo after excision from endosperm of 1-week-growth rice seed

source_name: Target (CH2) source: Callus-forming embryo treated with sugar-free status for 2 days


title: 2220_1_C0001_T0002

description:
Control (CH1): Dehusked and sterilized seeds of rice (Oryza sativa L. cv Akitakomachi) were put on agar and kept in dark for 2 days at 4 degreesC for swelling. Then, they were transferred to 28 degreesC keeping in dark. After 4 days, etiolated seedlings were under the far red light (FR) for 15 min and coleoptiles (1.5 - 2cm long) were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Dehusked and sterilized seeds of phyA mutant (osphyA-1) rice (Background: Oryza sativa L. cv. Akitakomachi) were put on agar and kept in dark for 2 days at 4 degreesC for swelling. Then, they were transferred to 28 degreesC keeping in dark. After 4 days, coleoptiles (1.5 - 2cm long) of etiolated seedlings were harvested for RNA extraction without any light treatment. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Photomorphogenesis, phyA mutant,

source_name: Control (CH1) source: Etiolated seedlings (4 days growing) of wild type exposuered under the FR light for 15 min

source_name: Target (CH2) source: Etiolated seedlings of phyA1 mutant


title: 2218_2_C0101_T0103

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown at glass house. Seed coat+remainding part of seed on 1 day after pollination were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were grown at glass house. Seed coat 3+6 day after pollination were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Metabolism, Tissue specificity, Seed coat

source_name: Target (CH2) source: Seed coat 3+6 day after pollination


title: 2221_1_C0001_T0002

description:
Control (CH1): Callus of NIL rice (Oryza sativa L. cv Koshihikari x Kasalath) including QTLa and QTLb (QTLa and QTLb: the both loci for Kasalath showed culture characteristics of the Kasalath plant)  were cultured in liquid media for 5 days after 4 weeks since calli was initiated. The calli derived from scutellum of mature seed (less than 2mm in diameter) were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Callus of NIL rice (Oryza sativa L. cv Koshihikari x Kasalath) including QTLa (QTLa: the loci for Kasalath showed culture characteristics of the Kasalath plant) were cultured in liquid media for 5 days after 4 weeks since calli was initiated. The calli derived from scutellum of mature seed (less than 2mm in diameter) were harvested for RNA extraction. Extracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, , QTL, Culture characteristics

source_name: Control (CH1) source: Calli derived from scutellum of mature seed (QTLa&QTLb)

source_name: Target (CH2) source: Calli derived from scutellum of mature seed (QTLa)


title: 2218_1_C0001_T0001

description:
Control (CH1): Callus-forming embryo (50 micro gram /g fresh weight glucose) after excision from endosperm of 1-week-growth rice seed (Oryza sativa L. cv Notohikari) with 2,4-D that were harveted for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Callus-forming embryo of rice seed (Oryza sativa L. cv Notohikari) after excision from endosperm were grown with 2,4-D for 5 days. Then, they were trasfered to high sugar condition (90mM glucose). After 2 days treatment under high sugar condition, they were harveted for RNA extraction Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Metabolism, Sugar, Metabolism

source_name: Control (CH1) source: Callus-forming embryo after excision from endosperm of 1-week-growth rice seed (no treatment)

source_name: Target (CH2) source: Callus-forming embryo treated with high sugar status for 2 days


title: 2216_2_C0001_T0005

description:
Control (CH1): Leaves at 4th leaf stage of rice (Oryza sativa L. cv Nipponbare) were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Leaves at 4th leaf stage of triptophan accmuration-transgenic line (gene for anthranilate synthase alpha-subunit, OASA2 were tranformed) of rice (Oryza sativa L. cv Nipponbare) were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Transgenic, Anthranilate synthase alpha-subunit gene,

source_name: Control (CH1) source: Leaf at 4th leaf stage, non transformant

source_name: Target (CH2) source: Leaves at 4th leaf stage of OASA2 transformant (OASA2: anthranilate synthase alpha-subunit gene)


title: 2216_2_C0001_T0001

description:
Control (CH1): Leaves at 4th leaf stage of rice (Oryza sativa L. cv Nipponbare) were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Leaves at 4th leaf stage of triptophan accmuration-transgenic line (modified gene for anthranilate synthase alpha-subunit, OASA1D were tranformed) of rice (Oryza sativa L. cv Nipponbare) were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Transgenic, Anthranilate synthase alpha-subunit gene,

source_name: Target (CH2) source: Leaves at 4th leaf stage of OASA1D transformant  (OASA1D: modified anthranilate synthase alpha-subunit gene)


title: 2210_2_C0003_T0004

description:
Control (CH1): Stock plants (Matthiola incana L. cv Yukio), a member of Cruciferae, were grown in pots at 25 degreesC/20 degreesC (day/night) under a 12 hours photoperiod in phytotron. After growing for 6 weeks, the plants were treated twice every week with 10 mL of 50 ppm of uniconazol (UCZ), which is an inhibitor of gibberellin (GA) biosynthesis. The UCZ treated plants were, then, exposed to 10 degreesC of low temperature treatment without GA for 7 days, and total RNA was extracted from the shoot apex.
Target (CH2): Stock plants (Matthiola incana L cv Yukio), a member of Cruciferae, were grown in pots at 25 degreesC /20 degreesC (day_night) under a 12 hours photoperiod in phytotron. After growing for 6 weeks, the plants were treated twice every week with 10 mL of 50 ppm of uniconazol (UCZ), which is an inhibitor of gibberellin (GA) biosynthesis. The UCZ treated plants were, then, exposed to 10 degreesC of low temperature treatment with 10 mL of GA (10 mg mL-1) on the shoot apex for 2 weeks, and total RNA was extracted from the shoot apex.
Keyword: Rice microarray project, Rice 8987 EST array, GA, Temperature, Stock plants

organism: Matthiola incana

source_name: Control (CH1) source: Shoot apex of the plants treated without GA for 7 days under low tempearature condition  after Uniconazo

source_name: Target (CH2) source: Shoot apex of the plants treated with GA (10 mg/mL, 2 weeks) under low tempearature condition  after Unic


title: umuc3

description: Gene expression data from bladder cancer cell lines before drug treatment.

source_name: bladder cancer cell line


title: 2216_1_C0001_T0001

description:
Control (CH1): Leaves at 3rd leaf stage (1 week after seedlings) of rice (Oryza sativa L. cv Nipponbare) were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Leaves at 3rd leaf stage (1 week after seedlings) of triptophan accmuration-transgenic line (gene for anthranilate synthase, AS were tranformed) of rice (Oryza sativa L. cv Nipponbare) were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Transgenic, Triptophan accmuration, Anthranilate synthase

source_name: Control (CH1) source: Seedlings (leaf) at 3rd leaf stage of non-transgenic plants

source_name: Target (CH2) source: Leaves at 3rd leaf stage of Triptophan accmuration transgenic line


title: 2215_2_C0001_T0002

description:
Control (CH1): Rice (Oryza sativa L. cv Shiokari) were grown in a growth chamber at 30 degreesC in light for 10 hours and at 25 degreesC in dark for 14 hours. Total RNA was extracted from shoots on 16 days after sowed with an extraction reagent ISOGEN. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Shiokari) dwarf mutant ID30 were grown in a growth chamber at 30 degreesC in light for 10 hours and at 25 degreesC in dark for 14 hours. Total RNA was extracted from shoots on 16 days after sowed with an extraction reagent ISOGEN. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Dwarf mutant ,

source_name: Control (CH1) source: Shoots 16 days after sowed

source_name: Target (CH2) source: 16 days-shoots after sowed of Dwarf mutant ID30


title: 2216_2_C0001_T0003

description:
Control (CH1): Leaves at 4th leaf stage of rice (Oryza sativa L. cv Nipponbare) were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Leaves at 4th leaf stage of triptophan accmuration-transgenic line (gene for anthranilate synthase alpha-subunit, OASA1 were tranformed) of rice (Oryza sativa L. cv Nipponbare) were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Transgenic, Anthranilate synthase alpha-subunit gene,

source_name: Target (CH2) source: Leaves at 4th leaf stage of OASA1 transformant (OASA1: anthranilate synthase alpha-subunit gene)


title: 2217_1_C0001_T0003

description:
Control (CH1): Leaf sheath of the first leaf below the flag leaf at stage 1 (the rice plants, Oryza sativa L. cv Nipponbare, in heading stage were classified into seven developing stages depend on the length of panicle (P) and neck internode (I), and the fresh weight of each panicle (Pw) as follows: (1) P < 10 cm, (2) 10< P < 18 cm, (3) 18< P cm, (4) in heading, (5) Pw < 1.5 g, (6) 1.5 < Pw < 2.5 g, (7) 2.5 g < Pw.) were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Leaf sheath of the first leaf below the flag leaf at stage 7 (the rice plants, Oryza sativa L. cv Nipponbare, in heading stage were classified into seven developing stages depend on the length of panicle (P) and neck internode (I), and the fresh weight of each panicle (Pw) as follows: (1) P < 10 cm, (2) 10< P < 18 cm, (3) 18< P cm, (4) in heading, (5) Pw < 1.5 g, (6) 1.5 < Pw < 2.5 g, (7) 2.5 g < Pw.) were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Sink source, ,

source_name: Control (CH1) source: Leaf sheath of the first leaf at stage 1

source_name: Target (CH2) source: Leaf sheath of the first leaf at stage 7


title: 2205_2_C0201_T0201

description:
Control (CH1): GUS-transformant, T5 generation, of rice (Oryza sativa L. cv Tsukinohikari) were steririle germinated, then transplanted with paddy soil. After transplantation, the plants were grown in greenhouse at 28-30 degreesC for 2 weeks (light 15 hours/dark 9 hours). Young leaf from seedling of the plants were harvested for RNA extraction. Extracted mRNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): GUS-transformant, T5 generation, of rice (Oryza sativa L. cv Tsukinohikari) were steririle germinated, then transplanted with paddy soil. After transplantation, the plants were grown in greenhouse at 28-30 degreesC for 8 weeks (4 weeks in light 15 hours/dark 9 hours, 4 weeks in light 10 hours/dark 14 hours). Mature leaf at anthesis of the plants were harvested for RNA extraction. Extracted mRNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Gene silencing, beta-glucuronidase (GUS),

source_name: Control (CH1) source: Seedling (young leaf) of GUS-transformant

source_name: Target (CH2) source: Mature leaf at anthesis of GUS-transformant (GUS: beta-glucuronidase)


title: 2133_2_C0002_T0001

description:
Control (CH1): Suspension-cultured cell derived from germinating seed of rice (Oryza sativa L. cv Kakehashi) was incubated for 8 hours in phosphate buffer (pH6.0) added medium. Extracted total RNA from the cell were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Suspension-cultured cell derived from germinating seed of rice (Oryza sativa L. cv Kakehashi) was incubated for 8 hours in blast fungal elicitor added medium. Extracted total RNA from the cellwere labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Pathogen, Blast fungal elicitor ,

source_name: Control (CH1) source: Suspension-cultured cell derived from germinating seed incubated for 8 hours

source_name: Target (CH2) source: Suspension-cultured cell incubated for 8 hours in medium containing blast fungal elicitor


title: 2215_1_C0001_T0001

description:
Control (CH1): Proantcyanidin (polyphenol) synthesis mutant, ant13-152, of barley (Hordeum vulgare L. cv triumph) grown in a field. Total RNA was extracted from immature grains about 20 days after heading by ISOGEN. Purified mRNA using Dynabeads mRNA Direct Kit were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Proantcyanidin (polyphenol) synthesis mutant, ant17-148, of barley (Hordeum vulgare L cv triumph) grown in a field. Total RNA was extracted from immature grains about 20 days after heading by ISOGEN. Purified mRNA using Dynabeads mRNA Direct Kit were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Proantcyanidin (polyphenol) synthesis mutant, Barley

organism: Hordeum vulgare

source_name: Control (CH1) source: Immature grains of mutant, ant13-152, grown in a field.

source_name: Target (CH2) source: 20 days-immature grains after heading of mutant ant17-148


title: 2210_2_C0002_T0001

description:
Control (CH1): Stock plants (Matthiola incana L. cv Yukio), a member of Cruciferae, were grown in pots at 25 degreesC/20 degreesC (day/night) under a 12 hours photoperiod in phytotron. After growing for 6 weeks, the plants were treated twice every week with 10 mL of 50 ppm of uniconazol (UCZ), which is an inhibitor of gibberellin (GA) biosynthesis. The UCZ treated plants were, then, exposed to 10 degreesC of low temperature treatment without GA for 3 days, and total RNA was extracted from the shoot apex.
Target (CH2): Stock plants (Matthiola incana L cv Yukio), a member of Cruciferae, were grown in pots at 25 degreesC /20 degreesC (day/night) under a 12 h photoperiod in phytotron. After growing for 6 weeks, the plants were treated twice every week with 10 mL of 50 ppm of uniconazol (UCZ), which is an inhibitor of gibberellin (GA) biosynthesis. The UCZ treated plants were, then, exposed to 10 degreesC of low temperature treatment with 10 mL of GA (10 mg mL-1) on the shoot apex for 1 day, and total RNA was extracted from the shoot apex.
Keyword: Rice microarray project, Rice 8987 EST array, GA, Temperature, Stock plants

source_name: Control: Shoot apex of the plants treated without GA for 3 days under low tempearature condition  after Uniconazole treatment

source_name: Target: Shoot apex of plants treated with GA (10 mg/mL, 1 day) under low tempearature condition  after Uniconazole treatment


title: 2202_2_C0201_T0202

description:
Control (CH1): 7-day-old seedlings after germination of rice (Oryza sativa L. cv Nipponbare) transformed with pTA7001-cycOs4 (cycOs4: rice cyclin B2;2 gene) were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): 7-day-old seedlings after germination of rice (Oryza sativa L. cv Nipponbare) transformed with pTA7001-cycOs4 (cycOs4: rice cyclin B2;2 gene) were treated with 1 microM DEX for 20 hours. The whole plants were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Transgenic, cyclin B2;2, DEX

source_name: Control (CH1) source: 7-day-old seedlings transformed with pTA7002-cycOs4

source_name: Target (CH2) source: 7 days-seedling transformed with pTA7002-cycOs4 were treated with 1 microM DEX for 20 hours


title: 2207_1_C0001_T0001

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown at 28 degreesC to 25 degreesC in light and dark condition. Young panicles of the plants were harvested before 11days of the heading for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were grown at 28 degreesC to 25 degreesC in light and dark condition. Young panicles of the plants were harvested before 7 days of the heading for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Growth stage, Panicle,

source_name: Control (CH1) source: Young panicles harvested on 11days of the heading

source_name: Target (CH2) source: Young panicles before 7days of the heading


title: 2209_1_C0001_T0002

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown in the complete darkness. The 3rd leaves from etiolated seedlings grown in the darkness for 14 days were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were grown in the complete darkness. The 3rd leaves from etiolated seedlings grown in the darkness for 14 days were exposed to white light (150 micro mole/ m2 s) for 10 min, then were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Photomorphogenesis, White light,

source_name: Control: Whole plant (etiolate seedlings) grown in complete darkness for 14 days

source_name: Target: 3rd leaves from etiolated seedlings exposed to white light for 10min


title: 2207_2_C0001_T0001

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown at 28 degreesC to 25 degreesC in light and dark condition. Young panicles of the plants were harvested before 11days of the heading for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were grown at 28 degreesC to 25 degreesC in light and dark condition. Young panicles of low temperature treatment at 12 degreesC for 6 days at booting stage were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Low temperature, Panicle,

source_name: Control (CH1) source: Panicles before 11days of the heading

source_name: Target (CH2) source: Young panicles treated with low temperature (12 degreesC) for 6 days


title: 2205_1_C0001_T0001

description:
Control (CH1): Developed leaf at 7 days before heading of rice (Oryza sativa L. cv Tsukinohikari) were used for RNA extraction. Extracted mRNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Developed leaf at 7 days before heading of rice (Oryza sativa L. cv Tsukinohikari) GUS (beta-glucuronidase) silencing line were used for RNA extraction. Extracted mRNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Gene silencing, beta-glucuronidase (GUS),

source_name: Control (CH1) source: Leaf of non-transformant harvested on 1 week before heading

source_name: Target (CH2) source: Developed leaf of GUS (beta-glucuronidase) silencing line harvested on 7 days before heading of


title: 2204_2_C0001_T0001

description:
Control (CH1): Leaves before expansion of rice (Oryza sativa L. cv Nipponbare) as parental line for DNA hypomethylation rice 1-17 were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Leaves before expansion of rice (Oryza sativa L. cv Nipponbare) mutant T1, DNA hypomethylation rice 1-17(T1), were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, DNA modification, Mutant, Hypomethylation

source_name: Control (CH1) source: Leaves before expansion (parental line)

source_name: Target (CH2) source: Leaves before expansion of DNA hypomethylation rice (T1)


title: 2209_1_C0001_T0001

description:
Control (CH1): Rice (Oryza sativa L. cv Nipponbare) were grown in the complete darkness. The 3rd leaves from etiolated seedlings grown in the darkness for 14 days were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Rice (Oryza sativa L. cv Nipponbare) were grown in the complete darkness. The 3rd leaves from etiolated seedlings grown in the darkness for 14 days were exposed to red light (15 micro mole/ m2 s) for 15 min, then were harvested for RNA extraction. Exracted total RNA were  labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Photomorphogenesis, Red light,

source_name: Control (CH1) source: Whole plant (etiolate seedlings) grown in complete darkness for 14 days

source_name: Target (CH2) source: 3rd leaves from etiolated seedlings exposed to red light for 15min


title: 2201_1_C0001_T0002

description:
Control (CH1): The cell cycle of  rice Oc cells from rice seedling (Oryza sativa L. cv. Ghaiya) was synchronized using aphidicolin (5 micro gram /ml), and cells were collected at G1 phase. The collected cells were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): The cell cycle of  rice Oc cells from rice seedling (Oryza sativa L. cv. Ghaiya) was synchronized using aphidicolin (5 micro gram /ml), and cells were collected at G2 phase. The collected cells were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Cell cycle, G1/G2,

source_name: Control (CH1) source: Oc cells harvested in G1 phase (cells was synchronized using 5 microg/ml aphidicolin)

source_name: Target (CH2) source: Oc cells harvested in G2 phase (cells was synchronized using 5 microg/ml aphidicolin)


title: 2202_1_C0101_T0101

description:
Control (CH1): 10-day-old seedlings after germination of rice (Oryza sativa L. cv Nipponbare) transformed with pTA7001 (vector only) were treated with 1 microM dexamethasone (DEX) for 48 hours. Whole plant were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): 10-day-old seedlings after germination of rice (Oryza sativa L. cv Nipponbare) transformed with pTA7001-R2 (R2: CDK activating kinase) were treated with 1microM dexamethasone (DEX) for 48 hours. The whole plant used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Transgenic, CDK activating kinase, DEX

source_name: Control (CH1) source: 10-day-old seedlings of transformed with pTA7001 (vector only) that were treated with 1 microM DEX for 4

source_name: Target (CH2) source: 10 days-seedling transformed with pTA7001-R2 (R2: CDK activating kinase) treated with 1microM DEX for 48


title: 2204_1_C0001_T0002

description:
Control (CH1): Leaves of rice (Oryza sativa L. cv Nipponbare) were used for RNA extraction. Extracted mRNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Leaves of rice plant (Oryza sativa L. cv Nipponbare) T1 transformed with DDM1 antisense (DDM: decrease in DNA methylation) were used for RNA extraction. Extracted mRNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, DNA modification, DNA methylation, DDM1

source_name: Control (CH1) source: Leaf of plants

source_name: Target (CH2) source: Leaf of  DDM1 antisense (DDM: decrease in DNA methylation)


title: 2202_1_C0001_T0001

description:
Control (CH1): 10-day-old seedlings after germination of rice (Oryza sativa L. cv Nipponbare) transformed with pTA7001 (vector only) were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): 10-day-old seedlings after germination of rice (Oryza sativa L. cv Nipponbare) transformed with pTA7001-R2 (R2: CDK activating kinase) were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Transgenic, CDK activating kinase,

source_name: Control: 10-day-old seedlings transformed with pTA7001 (vector only)

source_name: Target: 10-day-old seedlings transformed with pTA7001-R2 (R2: CDK activating kinase)


title: 2133_1_C0001_T0001

description:
Control (CH1): Suspension-cultured cell of rice (Oryza sativa L. cv Kakehashi) were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Suspension-cultured cell of rice (Oryza sativa L. cv Kakehashi), lesion mimic mutant 2020, were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Lesion mimic mutant,

source_name: Control (CH1) source: Suspension-cultured cell

source_name: Target (CH2) source: Suspension-cultured cell of lesion mimic mutant


title: 2133_2_C0001_T0007

description:
Control (CH1): Suspension-cultured cell derived from germinating seed of rice (Oryza sativa L. cv Kakehashi) was incubated for 8 hours in phosphate buffer (pH6.0) added medium. Extracted total RNA from the cell were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Suspension-cultured cell derived from germinating seed of rice (Oryza sativa L. cv Kakehashi) was incubated for 8 hours in blast fungal elicitor and MAPK inhibitor (SB203580) added medium. Extracted total RNA from the cellwere labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Pathogen, Blast fungal elicitor , MAPK inhibitor

source_name: Control (CH1) source: Suspension-cultured cell derived from germinating seed incubated for 8 hours

source_name: Target (CH2) source: Suspension-cultured cell incubated for 8 hours in blast fungal elicitor and MAPK inhibitor (SB) added medium


title: 2130_2_C0301_T0302

description:
Control (CH1): Seeds of rice (Oryza sativa L. cv Nipponbare) were imbibed with water and germinated under the following conditions (50 microE m-2; 16 hours light / 8 hours dark cycle at 25 degreesC). Seeds were not submerged. The above ground part of seedlings harvested on 10 days after imbibition for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seeds of rice (Oryza sativa L. cv Nipponbare), dwarf mutant (Tanginbozu), were imbibed with 10 mM H2O2 solution and germinated under the following conditions (50 microE m-2; 16 hours light / 8 hours dark cycle at 25 degreesC). Seeds were not submerged. The above ground part of seedlings harvested on 10 days after imbibition for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Oxidative, Chlorine dioxide, Dwarf mutant (Tanginbozu)

source_name: Control (CH1) source: Seedling (above ground part) of dwarf mutant (Tanginbozu) harvested on 10 days after imbibition of seeds

source_name: Target (CH2) source: Seedling (above ground part) after seeds of dwarf mutant (Tanginbozu) were imbibed with 10 mM H2O2 soluti


title: 2130_2_C0001_T0001

description:
Control (CH1): Seeds of rice (Oryza sativa L. cv Nipponbare) were imbibed with water and germinated under the following conditions (50 microE m-2; 16 hours light / 8 hours dark cycle at 25 degreesC). Seeds were not submerged. The above ground part of seedlings harvested on 10 days after imbibition for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seeds of rice (Oryza sativa L. cv Nipponbare) were imbibed with 0.5 mM H2O2 solution and germinated under the following conditions (50 microE m-2; 16 hours light / 8 hours dark cycle at 25 degreesC). Seeds were not submerged. The above ground part of seedlings harvested on 10 days after imbibition for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Oxidative, Chlorine dioxide,

source_name: Control (CH1) source: Seedling (above ground part)  harvested on 10 days after imbibition of seeds in 0.5  mM H2O2 solution

source_name: Target (CH2) source: Seedling (above ground part) after seeds were imbibed with 0.5 mM H2O2 solution


title: 2130_2_C0102_T0101

description:
Control (CH1): Seeds of rice (Oryza sativa L. cv Nipponbare) were imbibed with 0.5 mM H2O2 solution and germinated under the following conditions (50 microE m-2; 16 hours light / 8 hours dark cycle at 25 degreesC). Seeds were not submerged. The above ground part of seedlings harvested on 10 days after imbibition for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seeds of rice (Oryza sativa L. cv Nipponbare), dwarf mutant (Tanginbozu), were imbibed with water and germinated under the following conditions (50 microE m-2; 16 hours light / 8 hours dark cycle at 25 degreesC). Seeds were not submerged. The above ground part of seedlings harvested on 10 days after imbibition for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Dwarf mutant (Tanginbozu),

source_name: Target (CH2) source: Seedling (above ground part) after seeds of dwarf mutant (Tanginbozu) were imbibed with water


title: 2130_2_C0201_T0202

description:
Control (CH1): Seeds of rice (Oryza sativa L. cv Nipponbare) were imbibed with water and germinated under the following conditions (50 microE m-2; 16 hours light / 8 hours dark cycle at 25 degreesC). Seeds were not submerged. The above ground part of seedlings harvested on 10 days after imbibition for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Hulled seeds of rice (Oryza sativa L. cv Nipponbare), dwarf mutant (Tanginbozu), were imbibed with water and germinated under the following conditions (50 microE m-2; 16 hours light / 8 hours dark cycle at 25 degreesC). Seeds were not submerged. The above ground part of seedlings harvested on 10 days after imbibition for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Mutant, Dwarf mutant (Tanginbozu),

source_name: Control: Seedling (above ground part) harvested on 10 days after imbibition of seeds in water

source_name: Target: Seedling (above ground part) after hulled seeds of dwarf mutant (Tanginbozu) were imbibed with water


title: 2210_1_C0001_T0001

description:
Control (CH1): Stock plants (Matthiola incana L. cv Yukio), a member of Cruciferae, were grown in pots at 25 degreesC/20 degreesC (day/night) under a 12 hours photoperiod in phytotron. After growing for 6 weeks, the plants were treated twice every week with 10 mL of 50 ppm of uniconazol (UCZ), which is an inhibitor of gibberellin (GA) biosynthesis. The UCZ treated plants were, then, exposed to 10 degreesC of low temperature treatment without GA for 2 weeks. After one day exposure returning to  25 degreesC/20 degreesC  again, total RNA was extracted from the shoot apex.
Target (CH2): Stock plants (Matthiola incana L cv Yukio), a member of Cruciferae, were grown in pots at 25 degreesC /20 degreesC (day/night) under a 12 hours photoperiod in phytotron. After growing for 6 weeks, the plants were treated twice every week with 10 mL of 50 ppm of uniconazol (UCZ), which is an inhibitor of gibberellin (GA) biosynthesis. The UCZ treated plants were, then, exposed to 10 degrees C of low temperature treatment for 2 weeks with 10 mL of GA (10 mg mL-1) on the shoot apex. Total RNA was extracted from the shoot apex at the end
Keyword: Rice microarray project, Rice 8987 EST array, GA, Temperature, Stock plants

source_name: Control: Shoot apex of the plants treated without GA for 2 weeks under low tempearature condition after Uniconazole treatment

source_name: Target: Shoot apex of plants treated with GA (10 mg/mL, 2 weeks) under low tempearature condition  after Uniconazole treatment


title: 2131_1_C0001_T0002

description:
Control (CH1): Seedlings of rice (Oryza sativa L. cv Nipponbare) were grown at 28 degreesC for 8 days {day 1 to 6 in light, day 7 to 8 (48 hours) in dark} without submerged (0 hour). Shoot part of the plant were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seedlings of rice (Oryza sativa L. cv Nipponbare) were grown at 28 degreesC for 8 days {day 1 to 6 in light, day 7 to 8 in dark with low temperature condition (4 degreesC)}. Shoot part of the plant were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Low temperature, ,

source_name: Control (CH1) source: 8-day-old shoot of seedling (control)

source_name: Target (CH2) source: 8-day-old seedlings (shoot) treated with low temperature condition for 48 hours (4 degreesC)


title: 2129_2_C0201_T0202

description:
Control (CH1): Maize (Zea mays L. cv. Alice) plant were grown hydroponically at normal condition for 9 day. Root of the plant were harvested on 20 days after sowing for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Maize (Zea mays L. cv. Alice) plant, ys3 mutant, were grown hydroponically at normal condition for 9 day. Root of the plant were harvested on 20 days after sowing for RNA extraction. The recessive yellow stripe3 (ys3) mutation causes yellowing of tissue between the lateral veins, which is symptomatic of an iron deficiency. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Nutrient, Yellow stripe3 (ys3) mutat, Maize

organism: Zea mays

source_name: Control (CH1) source: Root (at hydroponics for 20 days after sowing) grown  at normal condition for 9 day (control)

source_name: Target (CH2) source: Root (20 days after sowing) of ys3 mutant


title: 2130_1_C0001_T0002

description:
Control (CH1): Seeds of rice (Oryza sativa L. cv Nipponbare) were imbibed with water and germinated under the following conditions (50 microE m-2; 16 hours light / 8 hours dark cycle at 25 degreesC). Seeds were not submerged. Seedling (above ground part) of the plants were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seeds of rice (Oryza sativa L. cv Nipponbare) were imbibed with with 1 mM H2O2 solution and germinated under the following conditions (50 microE m-2; 16 hours light / 8 hours dark cycle at 25 degreesC). Seeds were not submerged. Seedling (above ground part) of the plants were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Oxidative, Chlorine dioxide,

source_name: Target (CH2) source: Seedling (above ground part) after seeds were imbibed with 1 mM H2O2 solution


title: 2131_2_C0003_T0007

description:
Control (CH1): Seedlings of rice (Oryza sativa L. cv Nipponbare) were grown at 28 degreesC for 10 days without submerged (0 hour). Shoot part of the plant were used for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Target (CH2): Seedlings of rice (Oryza sativa L. cv Nipponbare) were grown at 28 degreesC for 10 days with submerged condition (48 hours). Shoot parts of the plant were harvested on 24 hours after released from submerged conditions for RNA extraction. Extracted total RNA were labeled by Cy5, and hybridized to the Rice 8987 EST microarray according to the protocols of reference (Yazaki J et al DNA Res. 2003; 10 :249). We calculated the expression ratio that applied to PRIM filtering and median normarization after dividing the signal intensity of RNA from traget plant by the signal intensity of that from control plant according the protocol of above reference.
Keyword: Rice microarray project, Rice 8987 EST array, Anerobic, ,

source_name: Control (CH1) source: 10-day-old shoot of seedling (control)

source_name: Target (CH2) source: 10-day-old seedlings (shoot) submerged for 48 hours